> My CloneDVD output directory includes the proper video and audio/subtitles that I selected, but the size of the VOB files is 3.99 gig in the directory. Should I infer that everything was just ripped and nothing was downsampled? <
Correct. No transcoding was done. Video & your Audio streams only add to 3.99 gig. CloneDVD doesn't make it bigger.
> Or did CloneDVD downsample the video based on the original quality estimate of 96% before the above mentioned audio tracks were removed? <
Of course not - that would be very stupid.
The Quality bar shows the quality if all audio and subtitle streams would be selected.
If you deselect an Audio stream, video size & quality will be increased. Only the meter doesn't show this. (CloneDVD2 will have a second meter on the Audio / Subtitle selection page).